Polymerase chain reaction (PCR) amplification of a portion of the genome of both rapidly-growing mycobacteria and nocardia, followed by restriction fragment length polymorphism (RFLP) analysis of the amplification products, is being evaluated to assess the utility of these procedures for use in the diagnostic laboratory. The technique has already proven useful in providing preliminary identification of these organisms within a few days of organism isolation, as compared with the month or more required for conventional identification based on biochemical testing. In addition, these molecular procedures seem to allow more accurate discrimination among species and subspecies than is possible with biochemical testing. We are currently correlating results obtained with phenotypic methods with molecular methods. For the nocardia group, we are investigating the use of other primer pairs to assure that amplification of the portion of the genome with which we are working can indeed be obtained from all species in the genus Nocardia. For the rapidly-growing mycobacteria, results of the studies with this procedure have stimulated us to reassess the salt tolerance test, which is widely used to help with the phenotypic identification of these organisms. We have defined the optimal conditions for performing the salt tolerance test, and we have shown that even under the best of circumstances it does not have the discriminating power of the molecular methods.